CVR - Coronavirus Vaccines R&D Roadmap

Milestone
1.1.b

Sequencing capacity

In progress

Enhance global capacity to generate and share genomic data from SARS-CoV-2 and other human coronaviruses, particularly in low-resource settings, to inform global surveillance efforts.

Progress Highlights

Khoo 2025 proposed a set of considerations for establishing pathogen genomic surveillance systems in low-resource settings, although quantifying the exact costs versus benefits of genomic surveillance is a challenge.

Wohl 2023 developed sample size calculations for variant detection and variant prevalence from whole-genome sequences based on the surveillance model; to determine whether low-resource countries are meeting the sample size requirement, sequence data from the Global Initiative for Sharing All Influenza Data (GISAID) EpiCoV database can be utilized.

Some tools developed earlier in the pandemic to monitor GISAID submissions automatically by country (CoVariants) or country income classification (FIND) are no longer being updated regularly; others that are updated regularly, such as Nextstrain Forecasts, are biased towards high income countries that meet sequence volume requirements

Several studies from low or lower middle income countries have been published over the past few years indicating that sequencing capacity exists, but the data are so retrospective that the variants described are no longer in circulation at the time of publication, and therefore cannot inform timely global surveillance efforts.